Which neural network architectures are there that perform 3D convolutions?
There are many approaches for training CNN on 3d data, but the decision to use a particular architecture is heavily dependant upon the format of your dataset.

If you are using 3d point cloud data, I would suggest you go through PointNet and PointCNN.

But training a CNN on 3d point clouds is very tough.

There is also a way to train CNNs by posing the 3d structure from different viewpoints (Multiview CNNs).

But remember that training CNN on 3d data is really a tough task. 

If you plan to use a voxelized input data format, I suggest going through VoxelNet.

Since you are mentioning deconvolution, the most relevant paper I can come across is 3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation.

But deconvolution in its own right is a very expensive operation, which acting on 3d data makes it very hard, so I would suggest you check for alternate methods.